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Evolution and genetics of adaption Flashcards

1
Q

Adaption definition

A

A characteristic that enhances the survival of reproduction of organisms that bear it, relative to alternative states

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2
Q

What does the hardy weinburg equation describe

A

The genetic allele frequency in a population that is not evolving

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3
Q

What does the Hardy weinburg equation predict

A

The genotype and allele frequencies in one generation from the allele frequencies in the previous generation

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4
Q

What are the assumptions of the hardy weinburg equation

A

No selection, no mutation and large population, random mating

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5
Q

What is the hardy weinburg equation

A

p^2 + 2pq+ q^2 = 1

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6
Q

Whats the usefullness of the hardy weinburg equation

A

Gives a null model

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7
Q

What 4 evolutionary forces are needed to disrupt the hardy weinburg equation

A

Random mutations, genetic drift, Migration between species and isolated populations and natural selection

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8
Q

Natural selection definition

A

Differerntial survival and or reproduction of individuals/ any group of reproductive units

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9
Q

How do you work out the fitness of a species

A

Probability of survival x average number of offspring for a class of individuals

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10
Q

Whats the maximum fitness

A

w=1

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11
Q

Whats the selection coefficient

A

The difference between w and 1

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12
Q

How do we know natural selection exists?

A

Correlations between trait and environment, responses to experimental change in the enviornment, coreelations between trait and fitness component, signatures in the genome

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13
Q

What are the problems with detecting selection?

A

Genetic drift can spread traits, ancestral state, selection might not cause any change, selection might not be working at the individual level, linkage

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14
Q

What does natural selection not do?

A

Always lead to adaptation, produce perfection, always progress, produce a balanced, harmonious world, consider ethics

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15
Q

What is the levels of standing genetic variation

A

Presence of alternative forms of a gene and giving lockers of a population

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16
Q

What do the levels of standing genetic variation predict

A

A species ability to adapt

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17
Q

What are some of the processes responsible for generating diversity

A

Mutation, sex, ploidy, balancing selection

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18
Q

What kind of mutations are passed on to the next generation

A

Germ line

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19
Q

What do germ line mutations include

A

Point mutations such as substitution, insertion, deletion and inversion

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20
Q

What mutations do not lead to changes

A

Synonymous and silent

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21
Q

What are some examples of Non-synonymous mutations

A

Missense, nonsense, frame change

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22
Q

Example of inversion mutations

A

Wading birds and their different male morphs: Independence, satellite and faeder

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23
Q

How do beneficial mutations arise?

A

Independent assortment, random fertilisation, crossing over, ploidy, balancing selection

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24
Q

What happens in independant assortment

A

Sexual reproduction mixes the DNA from the two haploid gametes to produce diploid offspring, when chromosomes line up, the chromosomes pull apart

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25
What happens in crossing over
Flailing chromosomes exchange genetic material between the chromosome pairs
26
What happens in ploidy
Diploid means two copies of everything, the rarer the recesive allele, the greater the degree of protection from natural protection
27
What are the two types of balancing selection
Heterozygote advantage and frequency dependant selection
28
What happens in heterozygote advantage and example
The heterozygote s fittest over dominance for example sick cell anaemia in Africa is beneficial for patients with malaria so is maintained in the population
29
What happens in frequency dependant selection and the two type
The rare alleles have the highest fitness. Postivie: fitness of a genotyoe goes up with its frequency- variation isnt maintained Negative: fitness of genotype goes down as its frequnecy goes up- maintains frequency
30
Example of frequency dependant selection
Cichlid feed by taking mouthfuls of fish of the sides- Controlled by a single gene
31
Polymorphism definition
Differences between individuals of the same species
32
Divergence definition
Differences between individuals of different species
33
Molecular evolutionary terms
Evolution is changes in allele frequencies over time a chromosome carries one possible allele at any given locus mutation generates a new allele which can be inherited by its carriers descendants Each new allele starts as a mutation in a single individual Frequency of the allele can increase or decrease in each passing generation
34
What can the starting frequency if the new mutation be calculated with
1/(2N) - n is the population of diploid individuals
35
Who proposed the neutral theory and when
Mootoo Kimura in 1968
36
What does the neutral theory hypothesise
The the fate of most mutations contributing to molecular is determined by drift rather than selection
37
What are the assumptions in the neutral theory
The mutations are either neutral or weakly selected
38
How do we measure DNA sequence variation
Single nucleotide polymorphisms (SNPS)
39
What does the Wright-Fisher model do
It makes explicitly, testable predications about patterns of polymorphism and divergence
40
What are the assumptions of the Wright-fisher model
random mating, no selective differences, new individuals are formed by sampling at random with replacement of gametes produced by individuals
41
What is the Wright- fisher model equation
E(pi) = 4NeU
42
Whats the importance of the Wright-fisher model
Gives us a way of explaining patterns of genetic diversity We can formally identify patterns of variation and use that to determine selective forces Species with larger population size and higher mutation rates tend to be more variable
43
What are commonly used neutral markers
Synonymous polymorphisms, silent polymorphisms
44
What does Ne stand for
effective population size
45
What are the effects of populations bottlenecks on Ne
Loss of variability due to genetic drift being more rapid in smaller populations Populations that experience bottlenecks are expected to have a low Ne
46
What do deleterious variants do
Tend to decrease in frequency in the population overtime tend to segregate at lower frequencies than neutral variants less likely to get fixed than neutral variants could linger in the population for a substantial amount of time
47
What do beneficial variants do
Tend to increase in frequency in the population Tend to segregate at higher frequencies than neutral alleles More likely to get fixed than neutral variants
48
What do small Ne lead to
Much weakened selection, leading to deleterious mutations drifting to high frequencies
49
What is it predicted that repeated bottlenecks lead to
Deleterious variants being more common in non-African populations
50
What are the mutations in synonymous polymorphisms likely to be
Most mutations are probably neutral
51
What are mutations in non- synonymous polymorphisms likely to be
They're likely to influence fitness
52
What is the rate of substitution equation under the rate of neutral molecular evolution
X= 2Nu x 1/(2N) = u
53
What does the rate of accumulation of new substitutions per generation depend on
The neutral mutation rate and independence of the population size
54
What is K
The expected number of substitutions per site between two homologous DNA sequences from two species
55
What is K proportional to
The mutation rate
56
What equation is used to estimate K
K = D/L D- the total number of differences L- the total number of sites considered
57
What does the neutral model predict in terms of time
Evolution should be constant over time since it depends only on the neutral mutation rate, u
58
What equation is used to predict mutation rate
T= K/ (2U)
59
What can patterns of point mutations be estimated using
Nucleotide substitutions
60
What are the feutures of the mammalian mitochondrial genome
Circular, double stranded DNA 15- 17 KB in length, 13 protein coding genes, 2 rRNA genes, 22 tRNA genes A control region
61
What is the relative rate test equation
Kxa= Kxb
62
What is the generation time effect hypothesis
Errors in DNA replication in germ line cells is a major source of mutation The hypothesis predicts a higher mutation rate per time unit in species with shorter generation time
63
How much of the human genome encodes for proteins
1%
64
How much of the human genome is conserved
5%
65
Characteristics of the tripartite motif protein
Primate genomes encode for defending themselves against retroviruses
66
What happened with the anti - malarial drug pyrimethamine
Introduced in 1970s, resistance spread to fixation in 6 years, it was induced by specific point mutations in active site of parasite
67
Why is population genetics needed?
Its not always clear what trait should be measured We need to rule out chance effect
68
What does Tajimas D do
Compares the relative abundance of intermediate and low frequency variatiants
69
What does D< 0 mean
An excess of intermediate frequency variants
70
How to make a linkage mapping cross
1. cross the two parental types 2. Cross the hybrid offspring 3. Recombination takes place during meiosis, shuffling the parental genomes around 4. The progeny of F1 cross, inheriting recombined parental genomes
71
How to genotype a mapping cross
Place genome markers at regular places across the genome that distinguish two parental types
72
How to determine where the casusative gene is
Perform a statistical test at regular intervals along each chromosome to test for an association with the trait
73
Examples of an extended phenotype
Innates to the animal e.g. burrowing behaviour of mice
74
What are skyscrapers in manhatton plots
Regions with genes that explain variation
75
What is the fixation index
The inbreeding in subpopulations (S) is relative to in the total population (T)
76
What did Sewall Wright propose
Inbreeding could be used as a measure of differentiation among subpopulations
77
What is the fixation index equation
Fst = (Ht- Hs)/Ht Hs: the average heterozygosity in the subpopulation H1 is the expected heterozygosity in the total population
78
Whats the scale for FST
0-1 O means no differentiation 1 is a fixed differentiation
79
What can we use to predict the gene flow
Nm (number of migrants in each generation)
80
How can we sample differentiation of genes
Microsatellites, SNPS, Sequencing whole genomes
81
What is involved in microsatellites
Repeats of 2-5 base pairs in non coding areas, can be amplified using PCR
82
Disadvantages and advantages with sequencing whole genome
More costly, more resolution, can detect bigger mutations
83
Example 1: Arabidopsis lyrate on serpentine soils
25 individuals from 4 populations, detected 8.4 million polymorphisms across the genome, 96 had allele frequency differences of greater than 80% between soil types
84
Why do small horns/ scurns persist when they have costs to male reproductive success
Horns is determined by many genes of small effect and are just an indicator of quality Genes associated with small horns confer a fitness advantage in females Genes associated with samll horns have some other benifit to males
85
What are the two social forms of fire ants
Monogynes: single queen Polygynes: multiple queens that are smaller
86
What are the two different forms of fire ants determined by
GP-9 gene
87
What is a super gene
A number of tightly linked genes that are not affected by recombination
88
What is cis-regulatory variation
Mutations/ regions that occur very close to the gene that the gene is regulating
89
What happens at the promoter of a gene
Where transcription is initiated, RNA will bind to that promoter to initiate transcription
90
What do enhancers do
Transcription factors bind and interact to the promoter and can be controlled by different enhancers
91
What happens post- transcriptionally
Alternative splicing, allows you to alter the sequence of the final protein, can remove exons after transcription or keep them to create different sequences of exons

Biology (9 decks)

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